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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA

Basic information

species Zea mays
transcript GRMZM2G125052_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 7
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
     |||  ||    |||| | |   | ||||   |  |   ||| || |  | |||    | ||    |||  | || ||| |   | |  |||  |  ||  ||||||||||||||||||  | |||||||||||||||||||| |||||||| ||| | |||||||||||||||||||  || || ||||||||||| ||||||||||
---gtatagtgcctctgcctatattcctctgtgcttactgctagtgatgaaattattgtccat-acgtgttacgctttc-aactaa--tgatcacc-tacctctgtttgaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA

upper sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 7
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgg-gtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
                      ||| |  |   | ||       |   || || | ||  || |||   ||     | | | ||  |  ||||||  | |      | |  |||| || ||||| ||||||||||||||  | | ||| |||||||| ||||| || ||||| ||||||||||||||||| || ||  ||||||| ||||| |
----------------------gtaca-ataaattcattaataagcattgaagttctt--ttatgaatttgg----tatatgactttaataaaaagtaaactctgatat--agGTGACCAAACCATTGTTGGAGACATCTCGGAAAGGATATCTTGCTGCAATATCTGCATCTAGTTACTCCTATGTTTCTTTACTCAAGCATTTTCTTCCAA

upper sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G05990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
      ||  | |||||  | |  ||   ||  | |||   |||   ||          |||| | ||     |||  ||||   | ||      |||||||   |||  |||| |  |||||| |  ||||||||||||| | ||||||||| || || || || || ||||||||||||| |||||| |||||   |||||| || || |
-----gtagagaactcg--tatcgattattggttacagtaagtgcattgtg--------ttgt-atacaaactatttcctaatggtgtt------cacatgtgggttt--agGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATCTCTGCTTCGAGTTACTCCTTTGTTTCCTTGCTGAGGCATTTTCTGCCAA

upper sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 7
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
                                || | |      ||||   | | ||    ||   ||  | |||| |   ||  |   |  || ||  | | |  |   |||| || || ||| ||||||||||||| |||| ||| |||||||||||||| || ||||| ||||||||||| ||||| || ||  ||  |||| ||||||
--------------------------------gtactgttttgctggttgtgatcttatcagttg-accattcattttggtactttacaagtaaacatctcttaaat---agGTGACCAAGCCTCTGTTGGAGACATCCAGAAAAGGTTATCTTGCGGCAATATCTGCATCAAGTTACTCCTACGTTTCTTTACTCAAGTGTTTCATTCCTA

upper sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 7
gtacaatatcgcactcgcctgtgt-atatgtgtgtgcagcgggtgtg-gtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
          |   |  ||  | | | ||   | ||     ||| |  ||    ||||  |    | | | |||     | || ||| |  |||  ||| |           |||| || |||||  |  |||||||||||||||  || |||||||| || ||||| ||||| ||||| |||| |||||| |||||  |||||||||| || |
----------gtcttttccaatttgacattcttatgtttttggtttatgtttttctttcaccctggtctccgta-----tttagccaacaaaaattccatacac--------agGTCACCAAACCACTCCTGGAGACATCAAGAAAGGGATATCTTGCAGCTATTTCTGCATCAAGTTATTCCTTTGTTTCTTTGCTCAAGCATTTCCTCCCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 4

GAAGTTGTTGAATCAGTGAAGAATGATTTTGGCAGCATTGACATACTAGTGCACTCTCTTGCTAATGGCCCAGAGgtacaatatc ... cattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA
                   gtctaac  putative branch site (score: 4)
                                            tcatttt  putative PPT
                           atcttaaaaa  TA-rich tract